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Fig. 1 | BMC Bioinformatics

Fig. 1

From: antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization

Fig. 1

Schematic Terrain Graph Starting from a vertice v , n subsequent vertices within the graph are visited by a single ant during its walk through the terrain in order to assemble an RNA sequence. For each visited vertex, a corresponding nucleotide information is incorporated to the corresponding position within the sequence. The specific vertex of position j is chosen probabilistic according to the set of edges leading away of the current vertex i. Hereby specific pheromone and terrain contributions of the edges influence the probabilities per position. The interplay of an increasing sequence constraint specificity and the applied inductive structure constraint determine the number of vertices for some sequence positions. For example, even though position m is labeled with an ‘N’ as sequence constraint, the position only has three vertices due to the sequence constraint of position 2 and its request to form a base pair with the nucleotide at position m. This leads to the removal of the ‘A’ nucleotide vertex in m, since this cannot base pair with neither ‘C’ nor ‘G’ at position 2

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